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Plant Cell. 2017 Oct;29(10):2336-2348. doi: 10.1105/tpc.17.00521. Epub 2017 Oct 12.

De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing.

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Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany.
Commissariat à l'Energie Atomique et aux Energies Alternatives, Genoscope, 91057 Evry, France.
Wageningen Plant Research, 6708 PB Wageningen, The Netherlands.
Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52428 Jülich, Germany.
Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.
C.M. Rick Tomato Genetics Resource Center, Department of Plant Sciences, University of California, Davis, California 95616.
URGI, INRA, Université Paris-Saclay, 78026 Versailles, France.
Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892.
The Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany


Updates in nanopore technology have made it possible to obtain gigabases of sequence data. Prior to this, nanopore sequencing technology was mainly used to analyze microbial samples. Here, we describe the generation of a comprehensive nanopore sequencing data set with a median read length of 11,979 bp for a self-compatible accession of the wild tomato species Solanum pennellii We describe the assembly of its genome to a contig N50 of 2.5 MB. The assembly pipeline comprised initial read correction with Canu and assembly with SMARTdenovo. The resulting raw nanopore-based de novo genome is structurally highly similar to that of the reference S. pennellii LA716 accession but has a high error rate and was rich in homopolymer deletions. After polishing the assembly with Illumina reads, we obtained an error rate of <0.02% when assessed versus the same Illumina data. We obtained a gene completeness of 96.53%, slightly surpassing that of the reference S. pennellii Taken together, our data indicate that such long read sequencing data can be used to affordably sequence and assemble gigabase-sized plant genomes.

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